Hi, John,
Thanks for the explanation. That really helps. I just loaded the realign
parameters into Matlab and found that all fMRI were realigned to the first
image in each session. By the way, where do you save the realign parameters
between first images in each session? Thanks again.
Yanjun
-----Original Message-----
From: John Ashburner [mailto:[log in to unmask]]
Sent: Monday, November 26, 2001 12:42 PM
To: Xu, Yanjun; [log in to unmask]
Subject: Re: fMRI realignment
> We have 5 runs fMRI for each subject, which were taken continously with
> short break ( a couple of minutes) at the same time. Each run has around
> 128 frames. When I run the realignment, I entered 5 sessions for each
> subject. As the result, all the fMRI frames are aligned to the first frame
> in each run. We need all the fMRI for the subject aligned to the same
> baseline frame so that we can do an analysis on all of them. So should I
> realign all the fMRI as one session? Or is there any other alternative?
Whe I wrote the SPM99 realignment code, I was working on the assumption
that there is less residual difference within session, than there is between
sessions, and that people will normally model session differences in their
design matrix. For this reason, the way the fMRI realignment works for each
subject is:
For each session, realign all images within the session to
match the first image of the session.
Then align all the sessions together by aligning all the first
images to match the first image of the first session.
As the algorithm stands, the result should be that all a subject's images
are aligned to the first image of the first session.
Best regards,
-John
--
Dr John Ashburner.
Functional Imaging Lab., 12 Queen Square, London WC1N 3BG, UK.
tel: +44 (0)20 78337491 or +44 (0)20 78373611 x4381
fax: +44 (0)20 78131420 http://www.fil.ion.ucl.ac.uk/~john
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